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Evgeny Kvon

@evgenykvon.bsky.social

Assoc Prof at University of California, Irvine. Genetics, Genomics, Gene Regulation, Development. Views are my own. https://www.kvonlab.org/

88 Posts1682 Follower549 Folgt
Jesse Engreitz@jengreitz.bsky.social · 2d ago

Systematic mapping of enhancers, silencers, and topological elements using prime editing deletion screens www.biorxiv.org/content/10.6... Check out our preprint on next-generation tech for mapping distal regulatory effects! We’re excited to help set this up - please get in touch Thread 👇

Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens

Noncoding regulatory elements in the human genome can control gene expression through distinct mechanisms, including acting as enhancers, silencers, or topological elements. However, we lack tools to ...

biorxiv.org

Shawn Cai@xshawncai.bsky.social · 2d ago

Have you ever looked at a gene in IGV or a genome browser and wondered “What are all those (ATAC-seq/H3K27ac/CTCF ChIP-seq/…) peaks doing?” 🤔 I’m thrilled to share that we developed a new technology called Swap-seq to answer that exact question. Swap-seq: www.biorxiv.org/content/10.6...

Evgeny Kvon@evgenykvon.bsky.social · 2w ago

This is a really cool finding, congrats! It also reminds me of a recent paper from John Lis's lab showing that LTR promoter transcription in the NMU enhancer attenuates its activity: pubmed.ncbi.nlm.nih.gov/42468524/. So it appears to be a broader mechanism?

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pubmed.ncbi.nlm.nih.gov

Philippe Batut@philippebatut.bsky.social · last mo.

🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇

Meng Zhu@zhumeng123.bsky.social · 2w ago

Two years since the 1st submission, our work on limb heterochrony is finally out! 🎉🎊 @cellcellpress.bsky.social Delayed hindlimb dev vs forelimb is a widely conserved trait in mammals. We show that maternal O2 regulates this phenotype 👉🏻 shorturl.at/MGrwl

Shifts in embryonic oxygen levels cue heterochrony in limb initiation

Mammalian embryos see a substantial increase in available oxygen once the placenta forms. This increase in oxygen exposure serves as a trigger for initiating the development of the hindlimb, thus cont...

shorturl.at

Evgeny Kvon@evgenykvon.bsky.social · 3w ago

G&D was the journal that made me fall in love with developmental genetics in college. Incredibly lucky my first grad paper was published there. Terri was the editor and accepted it after the 1st round which gave me so much optimism starting out. We’re lucky to have had her. RIP

Benoit Bruneau@benoitbruneau.bsky.social · 3w ago

sad to learn that Terri Grodzicker has passed. She was the founding editor of @genesdev.bsky.social and instantly made it a phenomenally important journal. Over 35 years as editor she brought the most important science to an eager audience. It is rare to find someone with such a breadth of knowledge

Wendy Bickmore@wbickmor.bsky.social · last mo.

It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...

Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics

This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...

nature.com

Rada-Iglesias Lab@radaiglesiaslab.bsky.social · last mo.

Have you ever wondered why developmental genes are often regulated by enhancers located at long distances? In this @natgenet.nature.com perspective, we speculate that long-range enhancer positioning may provide regulatory properties essential for proper gene expression www.nature.com/articles/s41...

Mechanisms and functional implications of long-range enhancer-dependent gene regulation - Nature Genetics

Development depends on gene regulation by enhancers across long genomic distances. This Perspective discusses mechanisms enabling long-range enhancer–promoter communication and the potential advantage...

nature.com

Evgeny Kvon@evgenykvon.bsky.social · 2mo ago

Breakthroughs like this rely on standing on the shoulders of giants. Beyond new DL models, this work was only possible thanks to high-quality epigenomic #ENCODE datasets and massive VISTA collection of validated enhancers built over 20+ years by @axelvisel.bsky.social, Pennacchio and Rubin labs.

Shenzhi Chen@shenzhichen1999.bsky.social · 2mo ago

Excited to share our paper in @natgenet.nature.com on the de novo design of tissue-specific mammalian enhancers that function in vivo in mouse embryos. 🧬🐭 www.nature.com/articles/s41...

Elzo de Wit lab @ NKI@dewitlab.bsky.social · 2mo ago

Not everything was done in cancer cell lines. Our original observation: www.nature.com/articles/nat... (note that we did not call them SEs back then, but the TF clusters are very similar) was in mESCs. Observations in GAM from the Pombo group were also on mESCs.

The pluripotent genome in three dimensions is shaped around pluripotency factors - Nature

Using 4C technology, higher-order topological features of the pluripotent genome are identified; in pluripotent stem cells, Nanog clusters specifically with other pluripotency genes and this clustering is centred around Nanog-binding sites, suggesting that Nanog helps to shape the three-dimensional structure of the pluripotent genome and thereby contributes to the robustness of the pluripotent state.

nature.com

Evgeny Kvon@evgenykvon.bsky.social · 2mo ago

“Super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting” www.cell.com/cell-genomic...

Single-cell 3D genome imaging shows super-enhancer hubs are rare, nonspecific, and neither necessary nor sufficient for transcriptional bursting

Super-enhancers have been proposed to cluster in the nucleus when compared to other genomic elements. Le et al. found that super-enhancer clustering was rare and driven by non-specific interactions. P...

cell.com

Evgeny Kvon@evgenykvon.bsky.social · 2mo ago

A really cool preprint from Joanna Wysocka's lab showing that housekeeping genes use distal enhancers as dosage buffers against TF fluctuations, but only during critical cell fate transitions. Makes so much sense! www.biorxiv.org/content/10.6...

Enhancer buffering protects dosage-sensitive housekeeping genes during vulnerable developmental transitions

Housekeeping genes maintain robust expression across cell types despite dynamic transcription factor fluctuations, yet their haploinsufficiency is associated with many tissue-specific developmental di...

biorxiv.org

Jay Shendure@jshendure.bsky.social · 2mo ago

Thrilled to post thread re: new single-cell lineage of mouse embryo reconstructed w/ DNA Typewriter. One animal, zygote to late organogenesis (E13.5). Tree has 1,340,794 transcriptionally profiled, annotated tips (cells), 1,142,588 dated internal nodes, rooted at zygote 1/n

Jeff Groh@jeffgroh.bsky.social · 3mo ago

Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...

Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

pnas.org

Cell - a Cell Press journal@cp-cell.bsky.social · 3mo ago

Now online! Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context

Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context

Using an in situ genome-rewriting platform, Zhou et al. demonstrate that precise transcriptional regulation of the NMU promoter is governed by a 3D regulatory hub comprising a core retroviral LTR enhancer, a decoy LTR promoter, and activity-boosting “facilitator” elements.

dlvr.it

Anders Sejr Hansen@andersshansen.bsky.social · 3mo ago

@mileshuseyin.bsky.social and the lab have put together a comprehensive protocol for genome-wide Micro-C and for Region-Capture Micro-C in @natprot.nature.com : www.nature.com/articles/s41... See also the GitHub for a user-friendly end-to-end computational pipeline: github.com/ahansenlab/M...

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Nature Protocols@natprot.nature.com · 3mo ago

New Article! Mapping 3D genome organization at nucleosome-scale with Micro-C and Region Capture Micro-C (RCMC)

Job Dekker@jobdekker.bsky.social · 3mo ago

Frank Grosveld has been a giant in the field of long-range gene regulation. Inspirational to me and I am sure for many others. Rest in peace.

Lluis Montoliu@lluismontoliu.bsky.social · 4mo ago

Frank Grosveld, born in 1948, passed away last Friday. He was a colossal scientist in the transcriptional control of gene expression during development and helped us understand the complex regulation of beta-globin genes. His work will remain as a reference. May he rest in peace.

Andrew Marderstein@amarderstein.bsky.social · 4mo ago

Our latest is out in Nature Genetics with @soumyakundu.bsky.social @anshulkundaje.bsky.social and @sbmontgom.bsky.social ! We built a resource of predicted variant effects on chromatin accessibility, and FLARE to identify disease variants with extreme effects. www.nature.com/articles/s41...

Decoding common and rare noncoding variant effects across cellular and developmental contexts - Nature Genetics

This study contributes a resource of predicted effects of noncoding variants on chromatin accessibility and a method to identify noncoding variants with extreme regulatory effects, with application to...

nature.com